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I-TASSER results for job id Rv1989c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.11 7 3s1wA GOL Rep, Mult 22,38,39,40,119,144,146,168,170
20.09 6 2fliA ZN Rep, Mult 38,40,58,170
30.05 3 1bosC UUU Rep, Mult 47,48,49
40.05 3 2z5xA DCX Rep, Mult 52,53,55,58
50.05 3 3a4xA UUU Rep, Mult 23,58,60,95,104,120,122,123,146,170
60.03 2 2fmoA FAD Rep, Mult 22,23,25,38,59,60,66,67,93,106,110,120,121,122,170
70.03 2 1iwpA PGO Rep, Mult 38,57,119,120,168
80.03 2 3s1uB E4P Rep, Mult 22,40,93,146,148,170,171,173
90.02 1 2o01J CLA Rep, Mult 69,72
100.02 1 1vh8B UUU Rep, Mult 40,44,47
110.02 1 2z5yA DCX Rep, Mult 48,55,58,59
120.02 1 2o66A FLC Rep, Mult 27,33

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.1931tqxA0.6603.540.0540.9035.1.3.1NA
20.1051xi3A0.6333.340.0690.8552.5.1.3NA
30.0793exrA0.6643.550.0820.9194.1.1.8561,63,68
40.0773f4wA0.6643.440.0650.9094.1.2.-24,41
50.0701xbzB0.6683.380.0890.9034.1.1.8561,65
60.0701xi3B0.6333.340.0690.8552.5.1.340,122,148
70.0692yw3E0.6303.420.1250.8604.1.2.1439
80.0681h1yA0.6483.640.0780.8925.1.3.192
90.0672yswA0.6443.910.0750.9254.2.1.10NA
100.0671h1yB0.6483.660.0710.9035.1.3.1NA
110.0671j2wA0.6333.530.0810.8664.1.2.4NA
120.0672yswC0.6413.940.0760.9194.2.1.10NA
130.0672cz5A0.6423.650.0360.8924.1.1.2361
140.0672v81A0.6323.430.0880.8554.1.2.21NA
150.0671vqtA0.5933.930.0440.8554.1.1.23NA
160.0672czfA0.6313.810.0360.9034.1.1.233,120,146
170.0671v5xA0.6133.620.1000.8505.3.1.2495
180.0672ox1D0.5974.120.0360.8764.2.1.10NA
190.0661hg3A0.6653.280.0670.8825.3.1.1NA
200.0662h6rB0.6383.570.0670.8765.3.1.1111
210.0602cksB0.6783.780.0890.9623.2.1.4NA
220.0601bqcA0.6763.700.0630.9353.2.1.78NA
230.0601dwaM0.6813.710.0720.9573.2.1.147NA
240.0603aboA0.6853.650.0390.9574.3.1.7121,169
250.0601dioA0.6803.730.0800.9464.2.1.28NA
260.0602gftB0.6744.170.0660.9793.2.1.89NA
270.0602pbgA0.6783.950.0560.9623.2.1.85NA
280.0601ybqA0.6763.900.0450.9623.4.19.161
290.0602j62A0.6774.050.0220.9733.2.1.52NA
300.0601qoxM0.6873.890.0720.9733.2.1.2125
310.0601tvnA0.6743.710.0510.9463.2.1.4NA
320.0602jf6B0.6783.870.0500.9683.2.1.10520
330.0602c8nA0.6933.820.0670.9683.2.1.5556
340.0601v03A0.6893.620.0670.9573.2.1.21NA
350.0601nvmA0.6873.700.0630.9464.1.3.38NA
360.0601onxA0.6773.890.0450.9623.4.19.-NA
370.0601myrA0.6833.680.0720.9573.2.1.147111
380.0601kwgA0.6763.490.0520.9193.2.1.23NA
390.0601eokA0.6733.980.0850.9413.2.1.96NA

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.290.6703.650.070.911dvjA GO:0003824 GO:0004590 GO:0006207 GO:0006221 GO:0008152 GO:0016829 GO:0016831 GO:0044205
10.120.6293.450.050.841lt7B GO:0000096 GO:0005737 GO:0005829 GO:0006479 GO:0006577 GO:0006579 GO:0008168 GO:0008270 GO:0008898 GO:0009086 GO:0016740 GO:0032259 GO:0042426 GO:0046500 GO:0046872 GO:0047150 GO:0050666 GO:0070062 GO:0071267
20.120.6783.590.080.945dmlA GO:0006974 GO:0008168 GO:0008652 GO:0008898 GO:0009086 GO:0016740 GO:0032259 GO:0033477 GO:0046872
30.110.6763.300.080.895dmnA GO:0006974 GO:0008168 GO:0008652 GO:0008898 GO:0009086 GO:0016740 GO:0032259 GO:0033477 GO:0046872
40.110.6773.590.090.924djdA GO:0005509 GO:0008168 GO:0015977 GO:0016740 GO:0031419 GO:0032259 GO:0042558 GO:0044237 GO:0046872 GO:0102036
50.110.5813.830.030.841umyD GO:0005737 GO:0005829 GO:0006479 GO:0006579 GO:0008168 GO:0008270 GO:0008898 GO:0009086 GO:0010243 GO:0016740 GO:0032259 GO:0032403 GO:0043234 GO:0046872 GO:0047150
60.100.6593.590.090.904cczA GO:0000096 GO:0005622 GO:0005737 GO:0005829 GO:0007399 GO:0008168 GO:0008270 GO:0008652 GO:0008705 GO:0008898 GO:0009086 GO:0009235 GO:0016740 GO:0031103 GO:0031419 GO:0032259 GO:0042558 GO:0044237 GO:0046872 GO:0048678 GO:0071732
70.100.6993.540.070.961q7qA GO:0008168 GO:0008705 GO:0009086 GO:0016740 GO:0031419 GO:0032259 GO:0042558 GO:0044237 GO:0046872
80.090.5903.120.060.753k13C GO:0005829 GO:0008168 GO:0008270 GO:0008705 GO:0008898 GO:0009086 GO:0016740 GO:0031419 GO:0032259 GO:0042558 GO:0044237 GO:0046872
90.090.6053.630.110.824o0qA GO:0042558 GO:0044237
100.080.6763.610.070.922yckX GO:0006760 GO:0008168 GO:0016740 GO:0032259 GO:0042558 GO:0044237
110.070.4555.180.080.774jjpA GO:0000166 GO:0005524 GO:0008972 GO:0009228 GO:0016301 GO:0016310 GO:0016740
120.070.4245.270.060.731ecfB GO:0000287 GO:0004044 GO:0005737 GO:0005829 GO:0006164 GO:0006189 GO:0006541 GO:0009113 GO:0009116 GO:0016740 GO:0016757 GO:0042802 GO:0046872
130.060.4224.920.050.691vjoA GO:0003824 GO:0008483 GO:0016740
140.060.3964.980.050.633ifsE GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
150.060.3915.450.050.703lhiA GO:0005975 GO:0006098 GO:0017057
160.060.3995.370.050.683ju7A GO:0003824
170.060.3485.710.060.655ez7A GO:0016491 GO:0055114
180.060.3635.610.070.634zrhF GO:0001922 GO:0002020 GO:0002237 GO:0002634 GO:0002677 GO:0003677 GO:0003824 GO:0004842 GO:0004843 GO:0005634 GO:0005737 GO:0005764 GO:0005829 GO:0006508 GO:0006915 GO:0006954 GO:0008152 GO:0008233 GO:0008234 GO:0008270 GO:0010803 GO:0016567 GO:0016579 GO:0016787 GO:0016874 GO:0019900 GO:0031397 GO:0032088 GO:0032480 GO:0032495 GO:0032691 GO:0032703 GO:0032715 GO:0032720 GO:0034136 GO:0034140 GO:0034144 GO:0034148 GO:0035871 GO:0036459 GO:0043124 GO:0043130 GO:0043621 GO:0045732 GO:0045736 GO:0045779 GO:0045824 GO:0046872 GO:0048662 GO:0050691 GO:0050727 GO:0050728 GO:0050869 GO:0051259 GO:0060548 GO:0061043 GO:0070062 GO:0070301 GO:0070423 GO:0070429 GO:0070433 GO:0070530 GO:0070536 GO:0070936 GO:0071108 GO:0071222 GO:0071947 GO:0072573 GO:0072666 GO:0090291 GO:1902042 GO:1903364 GO:2000347 GO:2000349 GO:2000352


Consensus prediction of GO terms
 
Molecular Function GO:0016830 GO:0046872 GO:0008898
GO-Score 0.59 0.39 0.31
Biological Processes GO:0006222 GO:0019856 GO:0033554 GO:0006790 GO:0032259 GO:0009086
GO-Score 0.59 0.59 0.43 0.43 0.39 0.31
Cellular Component GO:0005829 GO:0070062
GO-Score 0.12 0.12

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.